QLS GUEST SEMINAR - Wednesday 8 June

[Quantitative Life Sciences]

QUANTITATIVE LIFE SCIENCES GUEST SEMINAR

Wednesday, 8 June at 11:00

ICTP, Central Area, 2nd floor, old SISSA building

Title: " Protein Interactions: Integrating Computational Methods and 
Experimental Data for Understanding the Binding Specificity"

Speaker: M. Michael Gromiha - Department of Biotechnology, Indian 
Institute of Technology, Madras Chennai, India

Abstract:
Protein-protein interactions play crucial roles in many biological 
processes and responsible for smooth functioning of the machinery in 
living organisms. Predicting the binding affinity of protein-protein 
complexes and understanding the recognition mechanism are challenging 
problems in computational and molecular biology (1,2). We have developed 
a generalized energy based approach for identifying the binding site 
residues and interacting pairs in all types of protein complexes. We 
observed that the residues with charged and aromatic side chains are 
important for binding in protein-protein complexes. These residues 
influence to form cation–ππ, electrostatic and aromatic interactions. 
Our observations have been verified with the experimental binding 
specificity of protein-protein complexes and found good agreement with 
experiments (3). Further, we have developed algorithms for 
discriminating protein-protein complexes based on their binding 
affinities (4) and predicting the binding affinity (5). We suggest that 
our method would serve as an effective tool for identifying the 
interacting partners in protein-protein interaction networks and 
human-pathogen interactions based on the strength of interactions (6).
Recently, we have developed a protocol to identify the novel inhibitors 
for cYes kinase, which is a target for colorectal cancer using homology 
modeling, docking and virtual screening (7). The lead compounds have 
been verified with experiments, which show the inhibition rate of 30-70% 
and the IC50 in the range of 5-30 μM. The salient features of the 
results will be discussed.

References
1. M.M. Gromiha (2010) Protein Bioinformatics, Elsevier 
Publishers/Academic Press
2. M.M. Gromiha and K. Yugandhar (2016) Prog. Biophys. Mol. Biol. (in press)
3. M.M. Gromiha, K. Yokota and K Fukui (2009) Mol. Biosystems 5: 1779-1786.
4. K. Yugandhar and M.M. Gromiha (2014) Proteins. 82: 2088-96.
5. K. Yugandhar and M.M. Gromiha (2014) Bioinformatics.30: 3583-9.
6. K. Yugandhar and M.M. Gromiha (2016) Curr. Prot. Pept. Sci. 17, 72-81π
7. S. Chiba, K. Ikeda, T. Ishida, M.M Gromiha et al. (2015) Sci. Rep. 5, 
17209

Indico web page: http://indico.ictp.it/event/7895/



-- 
Erica Sarnataro
Group Secretary
Quantitative Life Sciences
The Abdus Salam International Centre for Theoretical Physics (ICTP)
Trieste,  Italy
Tel. +39-040-2240623
e-mail:qls at ictp.it